GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Caulobacter crescentus NA1000

Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate CCNA_01648 CCNA_01648 adenosylmethionine-8-amino-7-oxononanoate

Query= BRENDA::Q88RB9
         (425 letters)



>FitnessBrowser__Caulo:CCNA_01648
          Length = 420

 Score =  181 bits (459), Expect = 4e-50
 Identities = 121/350 (34%), Positives = 185/350 (52%), Gaps = 26/350 (7%)

Query: 25  PIFVDTAKNSTVIDVEGRELIDFAGGIAVLNTGHLHPKVVAAVQEQLTKVSHTCFQVLAY 84
           P+ V   + + +I  +GREL+D          G+ HP +  A+++Q+  + H  F  LA+
Sbjct: 27  PLPVVATRGARLILEDGRELVDGLASWWTACHGYNHPHIAGALRKQIETMPHVMFGGLAH 86

Query: 85  EPYVELCEKINKLVPGDFDKKTLLVTTGSEAVENAVKIA------RAATGRAGVIAFTGG 138
           EP   L +++ +L+PGD D       +GS AVE A+K+A      R   GR   +AF GG
Sbjct: 87  EPAYRLAKRLARLLPGDLDH-VFFAESGSVAVEIAMKMALQYQINRGVGGRTRFLAFRGG 145

Query: 139 YHGRTMMTLGLTG-KVVPYSAGMGLMPGGIFRALFPSELHGISVDDAIASVERIFKNDAE 197
           YHG T+ T+ +   +   +S   G+MP  +   L        ++D  +A         A 
Sbjct: 146 YHGDTLATMTVCDPEEGMHSLFAGVMPAQVIADLPRDPASEAALDALLA---------AR 196

Query: 198 PRDIAAIILEP-VQGEGGFLPAPKELMKRLRALCDQHGILLIADEVQTGAGRTGTFFAME 256
             +IAA+++EP +QG GG LP P E+++ LR L D+HG+LLI DE+ TG GRTG+ FAM+
Sbjct: 197 GHEIAAMLVEPLIQGAGGMLPHPPEVLRTLRRLADKHGVLLIFDEIFTGFGRTGSLFAMQ 256

Query: 257 QMGVAPDLTTFAKSIAGG-FPLAGVCGKAEYMDAI------APGGLGGTYAGSPIACAAA 309
             GV PD+ T +K++ GG  PL+    +    +A       A    G TY  +P+ACAAA
Sbjct: 257 AAGVEPDIVTLSKALTGGTLPLSAAVARRHVFEAFWSDDPAAALMHGPTYMANPLACAAA 316

Query: 310 LAVIEVFEEEKLLDRSKAVGERLTAGLREIQKKYPIIGDVRGLGSMIAVE 359
            A +++FE+         V   L  GL   +    ++ DVR LG++  VE
Sbjct: 317 NASLDLFEDGAWARDVARVSAALAEGLEPCRAGEGVV-DVRTLGAIGVVE 365


Lambda     K      H
   0.320    0.138    0.395 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 461
Number of extensions: 17
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 425
Length of database: 420
Length adjustment: 32
Effective length of query: 393
Effective length of database: 388
Effective search space:   152484
Effective search space used:   152484
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory